Variant report

Variant	rs554446857
Chromosome Location	chr5:154135474-154135475
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr5:154134135-154135991	ECC-1	luminal epithelium:	n/a	chr5:154135832-154135846 chr5:154134391-154134400 chr5:154135945-154135959
2	ZBTB7A	chr5:154134805-154136152	K562	blood:	n/a	n/a
3	TCF12	chr5:154133420-154136643	A549	lung:	n/a	chr5:154133494-154133502 chr5:154134317-154134324
4	MYC	chr5:154133822-154136192	K562	blood:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
5	TCF12	chr5:154134183-154135580	ECC-1	luminal epithelium:	n/a	chr5:154134317-154134324
6	PBX3	chr5:154134327-154135690	A549	lung:	n/a	n/a
7	SIN3AK20	chr5:154134213-154137170	PANC-1	pancreas:	n/a	n/a
8	E2F4	chr5:154134117-154135572	K562	blood:	n/a	chr5:154134136-154134145 chr5:154134202-154134212 chr5:154135302-154135311
9	POLR2A	chr5:154133143-154136943	K562	blood:	n/a	n/a
10	JUND	chr5:154135167-154137237	K562	blood:	n/a	chr5:154135300-154135309 chr5:154135301-154135310 chr5:154136541-154136550 chr5:154136802-154136816
11	HDAC2	chr5:154135100-154135488	K562	blood:	n/a	n/a
12	UBTF	chr5:154134102-154136984	K562	blood:	n/a	n/a
13	CHD1	chr5:154134917-154137347	GM12878	blood:	n/a	n/a
14	YY1	chr5:154135088-154136181	K562	blood:	n/a	chr5:154135832-154135846 chr5:154135945-154135959
15	POLR2A	chr5:154133745-154137338	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr5:154134782-154137071	GM12878	blood:	n/a	n/a
17	MYC	chr5:154134079-154136080	Hela-S3	cervix:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
18	POLR2A	chr5:154134809-154137109	GM12891	blood:	n/a	n/a
19	ZNF263	chr5:154135118-154139134	HEK293-T-REx	kidney:	n/a	chr5:154136788-154136809
20	TAF1	chr5:154134417-154135771	HepG2	liver:	n/a	n/a
21	MAZ	chr5:154134036-154137243	GM12878	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154134657-154134668 chr5:154134658-154134667
22	YY1	chr5:154134195-154136130	K562	blood:	n/a	chr5:154135832-154135846 chr5:154134391-154134400 chr5:154135945-154135959
23	HMGN3	chr5:154134186-154136077	K562	blood:	n/a	n/a
24	POLR2A	chr5:154135091-154137228	K562	blood:	n/a	n/a
25	ELF1	chr5:154133942-154137066	GM12878	blood:	n/a	chr5:154135952-154135964 chr5:154134375-154134387 chr5:154135789-154135802 chr5:154136215-154136227
26	SIN3AK20	chr5:154135463-154136410	MCF-7	breast:	n/a	n/a
27	POLR2A	chr5:154133940-154137103	K562	blood:	n/a	n/a
28	MYC	chr5:154133333-154137235	K562	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154133516-154133527 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154133517-154133526 chr5:154133518-154133525 chr5:154134657-154134668 chr5:154134658-154134667
29	MXI1	chr5:154132804-154137423	IMR90	lung:	n/a	n/a
30	POLR2A	chr5:154133358-154135811	HEK293	kidney:	n/a	n/a
31	POLR2A	chr5:154133873-154137159	K562	blood:	n/a	n/a
32	POLR2A	chr5:154134224-154137029	ProgFib	skin:	n/a	n/a
33	CTCF	chr5:154135319-154135488	GM19240	blood:	n/a	n/a
34	TAF1	chr5:154134220-154135554	HepG2	liver:	n/a	n/a
35	GATA3	chr5:154135201-154135607	T-47D	breast:	n/a	n/a
36	POLR2A	chr5:154134057-154137015	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr5:154133174-154137235	Raji	blood:	n/a	n/a
38	MXI1	chr5:154133886-154137235	GM12878	blood:	n/a	n/a
39	SIN3A	chr5:154133973-154138883	H1-hESC	embryonic stem cell:	n/a	chr5:154136477-154136488 chr5:154134277-154134290
40	POLR2A	chr5:154133868-154137145	K562	blood:	n/a	n/a
41	POLR2A	chr5:154134101-154137056	MCF-7	breast:	n/a	n/a
42	TCF7L2	chr5:154134029-154136089	HCT-116	colon:	n/a	n/a
43	POLR2A	chr5:154133576-154135735	HUVEC	blood vessel:	n/a	n/a
44	MYC	chr5:154133269-154135639	MCF10A-Er-Src	breast:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154133516-154133527 chr5:154134650-154134659 chr5:154133517-154133526 chr5:154133518-154133525 chr5:154134657-154134668 chr5:154134658-154134667
45	MYC	chr5:154133383-154137123	K562	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154133516-154133527 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154133517-154133526 chr5:154133518-154133525 chr5:154134657-154134668 chr5:154134658-154134667
46	POLR2A	chr5:154133080-154137254	K562	blood:	n/a	n/a
47	PAX5	chr5:154135057-154135586	GM12892	blood:	n/a	chr5:154135306-154135315
48	MYC	chr5:154133238-154137250	K562	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154133516-154133527 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154133517-154133526 chr5:154133518-154133525 chr5:154134657-154134668 chr5:154134658-154134667
49	MYC	chr5:154134130-154135541	MCF-7	breast:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
50	REST	chr5:154134025-154136593	H1-neurons	neurons:	n/a	chr5:154134277-154134290 chr5:154134592-154134605 chr5:154135833-154135846 chr5:154135770-154135783 chr5:154134736-154134749

No.	Distal block	Cell Line	Cell type
1	chr5:154135101..154137187-chr5:154183739..154185409,2	MCF-7	breast:
2	chr1:149857405..149859778-chr5:154134028..154135572,2	MCF-7	breast:
3	chr5:154059571..154067369-chr5:154132796..154138140,13	K562	blood:
4	chr5:154091014..154094062-chr5:154133007..154138054,7	MCF-7	breast:
5	chr5:154090008..154095548-chr5:154132332..154137735,10	MCF-7	breast:
6	chr5:154133833..154138436-chr5:154316104..154319386,7	K562	blood:
7	chr5:154133318..154137368-chr5:154208082..154212477,8	MCF-7	breast:
8	chr15:93351261..93351942-chr5:154134569..154135490,2	Hela-S3	cervix:
9	chr5:154059219..154066449-chr5:154131053..154139153,28	MCF-7	breast:
10	chr5:154092401..154094147-chr5:154134615..154136737,2	K562	blood:
11	chr5:154133591..154135701-chr5:179497285..179498805,3	MCF-7	breast:
12	chr5:154079413..154083903-chr5:154131964..154138437,9	MCF-7	breast:
13	chr5:154133224..154141155-chr5:154235246..154242227,24	MCF-7	breast:
14	chr17:59475759..59478103-chr5:154134019..154136422,2	MCF-7	breast:
15	chr5:154133665..154137234-chr5:154235811..154241105,6	MCF-7	breast:
16	chr5:154133563..154137747-chr5:154235219..154239187,9	K562	blood:
17	chr5:154134362..154135956-chr5:179498285..179499281,4	HCT-116	colon:
18	chr5:154134478..154136259-chr5:156568877..156571318,2	K562	blood:
19	chr5:154133598..154138734-chr5:154235660..154239806,12	K562	blood:
20	chr5:154133384..154135677-chr5:154316370..154317979,2	MCF-7	breast:
21	chr5:154133984..154137613-chr5:154316996..154320177,4	K562	blood:
22	chr5:154134637..154137206-chr5:154228501..154230611,2	MCF-7	breast:
23	chr5:154133720..154135863-chr5:154214585..154216471,2	K562	blood:
24	chr5:154134899..154136801-chr5:154190010..154191609,2	K562	blood:
25	chr2:241938134..241939654-chr5:154133580..154135809,2	K562	blood:

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000184270	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000155868	Chromatin interaction
ENSG00000082516	Chromatin interaction
ENSG00000113263	Chromatin interaction
ENSG00000263361	Chromatin interaction
ENSG00000221552	Chromatin interaction
ENSG00000135077	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000162804	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000263478	Chromatin interaction
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv3406300	chr5:154133209-154138557	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	esv3442367	chr5:154133259-154137657	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
4	esv3371359	chr5:154133784-154136632	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	esv3375024	chr5:154134009-154135957	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154133400-154137200	Active TSS	Lung	lung
2	chr5:154133600-154135800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:154133600-154137600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr5:154133800-154135600	Active TSS	Brain Germinal Matrix	brain
5	chr5:154133800-154137200	Active TSS	Esophagus	oesophagus
6	chr5:154133800-154137600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:154133800-154137600	Active TSS	Psoas Muscle	Psoas
8	chr5:154134000-154137600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:154134000-154137600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr5:154134000-154137600	Active TSS	Aorta	Aorta
11	chr5:154134000-154137600	Active TSS	Brain Anterior Caudate	brain
12	chr5:154134000-154137600	Active TSS	Brain Substantia Nigra	brain
13	chr5:154134000-154137600	Active TSS	Fetal Brain Female	brain
14	chr5:154134000-154137600	Active TSS	Fetal Kidney	kidney
15	chr5:154134000-154137600	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr5:154134000-154137800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:154134000-154137800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr5:154134000-154137800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr5:154134000-154138200	Active TSS	Ovary	ovary
20	chr5:154134000-154138400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:154134000-154138600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr5:154134200-154135600	Transcr. at gene 5' and 3'	Right Atrium	heart
23	chr5:154134200-154135800	Active TSS	Dnd41	blood
24	chr5:154134200-154137000	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr5:154134200-154137000	Active TSS	Spleen	Spleen
26	chr5:154134200-154137200	Active TSS	Gastric	stomach
27	chr5:154134200-154137600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:154134200-154137600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:154134200-154137600	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr5:154134200-154137600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr5:154134200-154137600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:154134200-154137600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:154134200-154137600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:154134200-154137600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:154134200-154137600	Active TSS	Brain Cingulate Gyrus	brain
36	chr5:154134200-154137600	Active TSS	Brain Hippocampus Middle	brain
37	chr5:154134200-154137600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr5:154134200-154137600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:154134200-154137600	Active TSS	Colon Smooth Muscle	Colon
40	chr5:154134200-154137600	Active TSS	Fetal Lung	lung
41	chr5:154134200-154137600	Active TSS	Fetal Stomach	stomach
42	chr5:154134200-154137600	Active TSS	Small Intestine	intestine
43	chr5:154134200-154137600	Active TSS	A549	lung
44	chr5:154134200-154137600	Active TSS	Hela-S3	cervix
45	chr5:154134200-154137800	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr5:154134200-154137800	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr5:154134200-154137800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr5:154134400-154137000	Active TSS	Primary B cells from peripheral blood	blood
49	chr5:154134400-154137000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr5:154134400-154137200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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